Are Delta Smelt Starving?

Posted on October 7, 2016 by Tom Cannon

The Sacramento Bee reported on August 31, 2016 that Dr. Ted Sommer at the California Department of Water Resources says that Delta smelt are starving. Dr. Sommer related recent success in stimulating the north Delta food web (Figure 1) by increasing flow through the Yolo Bypass in July as part of the state’s new strategy to help Delta smelt. I had reported earlier on the experiment and the strategy.

While Dr. Sommer was not implying that just adding some fertilizer to the north Delta would save the smelt, he was deflecting discussion and treatment away from the overriding cause of the collapse of Delta smelt: lack of spring-through-fall outflow to the Bay.

During August of this year, the normal heavy hand of Delta exports again reached out to degrade the critical habitat of what few smelt are left (Figure 2). In summer, Delta smelt concentrate near X2, the area of the estuary where brackish water of about 2 ppt salinity occurs. Food concentrates at X2, as shown in Figures 3 and 4. Chlorophyll levels at X2 are an order of magnitude higher than at Rio Vista (Figure 1), where Dr. Sommer observed the increase in chlorophyll from the recent experiment.

X2 also has cooler water temperatures and higher turbidities preferred by smelt (Figures 5 and 6). It is at X2 where smelt are meant to be so they do not starve, do not get eaten, and do not die from high water temperatures. The problem is that X2 habitat readily degrades when summer outflow is low (4000 cfs) and exports are high (11,200 cfs). Under these conditions, low-salinity habitat and food (plankton) are siphoned off with each tide into False River, into Dutch Slough, and further upstream into the San Joaquin River channel (also shown in Figure 2).

Smelt did fine in summer 2011, the year with the last decent fall smelt index. X2 was much further downstream, and Delta outflows were high (15,000 cfs). If X2 stays out of the Delta, and smelt can get to X2 and stay there, they and their food supply will be far better off. This requires about8,000-10,000 cfs outflow in July and 6,000-8,000 cfs outflow in August. The present 4,000 cfs outflow index (real outflow, as opposed to the index, is closer to zero – see Figure 2), while exports are11,200 cfs just does not meet their needs.

Figure 1. Chlorophyll concentrations at Rio Vista in the north Delta July 23 to August 31, 2016.

Figure 2. Net Delta hydrology (flow in cfs) on August 25/26 during a spring tide. Net Delta outflow is near zero with positive net flow in the Sacramento channel (north) and negative net flows in the San Joaquin channel (south). Exports were near maximum at 11,200 cfs. The location of X2 (2 ppt salt) at high tide is shown as magenta line.

Figure 3. Chlorophyll concentrations in summer 2016 at Blind Point in the lower San Joaquin channel (magenta line in Figure 2). Red circles denote periods when X2 moved upstream to Blind Point.

Figure 4. Salinity in summer 2016 at Blind Point in the lower San Joaquin channel (magenta line in Figure 2). Red circles denote periods when X2 approached Blind Point.

Figure 5. Water temperature in summer 2016 at Blind Point in the lower San Joaquin channel (magenta line in Figure 2). Red circles denote periods when X2 approached Blind Point.

Figure 6. Turbidity at Blind Point in the lower San Joaquin channel (magenta line in Figure 2). Red circles denote periods when X2 approached Blind Point.

Figure 7. Concentrations of Delta smelt in the Summer Townet Survey July 2011. Magenta line is location of X2.

My comments on: “SLDMWA Response to Environmentalists’ August 9, 2016 Request to the SWRCB for Even More Water Aimed at Protecting Delta Smelt”

Posted on September 15, 2016 by Tom Cannon

On August 11, Jason Peltier, executive director of the San Luis-Delta Mendota Water Authority, offered comments on a letter from environmental groups to the State Board that requested more water for Delta Smelt. Below, I provide some of Mr. Peltier’s statements, and a response to each:

1. “As environmental special interests request the State Water Resources Control Board expand failed policies on Delta Smelt, Californians are calling on the Board to implement new science-based, common sense approaches to protect the species. It is disheartening to see once credible environmental organizations calling for a “more of the same” approach – one that has so miserably failed for a quarter century – in a misguided attempt to help the imperiled delta smelt.”

Comment: The environmental organizations were proposing what the state has also offered as its new strategy for the Delta Smelt. It is not the old misguided “failed” strategy of diverting more and more water and providing less and less Delta outflow to the Bay. The state’s new strategy derives from some of the same actions suggested in this past April’s science workshop on Delta Smelt held at UC Davis, which Mr. Peltier attended.

2. “[t]he Projects have compensated for Mother Nature’s stinginess with water released from reservoirs, making the Delta far fresher than it would have been naturally.”

Fact: Just the “natural” summer inflow to Shasta Reservoir in the past four years of drought nearly equaled the amount allocated for summer Delta outflow. If you add up all the Central Valley’s “natural” inflow it would far exceed the Delta outflow allotted, even without accounting for use above the rim reservoirs.

3. “This dedication of water for fish from what was stored for drought relief has resulted in unprecedented socio-economic and environmental harms to towns, farms, and numerous species living in the largest wetlands in the West.”

Fact: Most of the water stored is for agriculture and released for agriculture. Mr. Peltier’s organization is simply last in line for stored water and thus gets less water allocated during droughts. In June and July, nearly 30,000 cfs of water was released on average from Central Valley reservoirs, but only 7000-8000 cfs reached the Bay to repel salt intrusion. Because Shasta releases were reduced to protect salmon (not smelt), Mr. Peltier’s organization was unable to receive more than a minimal allocation. Again, this is because its water rights are junior to those of other users, not because of water allocated to smelt (none).

4. “Since the most severe cuts were imposed on the Projects nine years ago, less water has been diverted, and thus more Projects’ water has gone out to the ocean, than at any other time in the past 35 years.”

Fact: Seven of the last nine years were drought years. The only water consistently reaching the ocean in large amounts during those seven years was uncontrolled river flows and reservoir spills during and after sporadic winter storms. The only reservoir water that reached the ocean (Bay) in those seven dry years was the water necessary to hold back salt intrusion into the Delta so Delta diversions and exports remained possible.

5. “Farmers, fishermen, and environmentalists – everyone that truly cares about the status of our imperiled fisheries – should be furious.”

Comment: The fishermen and environmentalists are “furious” because of government mismanagement of the Shasta Reservoir cold water pool that has nearly wiped out the Sacramento salmon runs, and because of the weakening of Delta water quality standards in 2014 and 2015 that allowed excess salt into the Delta and just about exterminated the Delta smelt population.

6. “Decades old state and federal policies have failed and brought delta smelt and salmon to the brink of extinction. The last thing we need is more of the same.”

Comment: Yes, decades-old policies of increasing exports from the Delta has brought near-extinctions. It started with the massive State Water Project that came on line in the 1970’s. Yes, the last thing we need is “more of the same” – increasing exports promised with the WaterFix.

7. “Like delta smelt, we need shelter, we need food, and we need safety from predators, toxics, and invasion. The state and federal regulatory agencies have ignored for far too long the full needs of delta smelt, only willing to do what is easy, and we have all suffered for it.”

Fact: Delta smelt need the cool, brackish, wind-blown turbid waters of Suisun Bay provided when Delta outflow is sufficient to keep the low salinity zone out of the warm, confined channels of the Delta and away from its massive export pumps.

8. “We can continue to ignore decades of sound scientific advice, or we can embark on a bold new initiative, one that is transparent and inclusive of stakeholders working with state and federal agencies to save delta smelt.”

Comment: We have ignored the scientific advice. It has always been there. What “bold new initiative?”

9. “Now is not the time for desperate action, it is the time for thoughtful action.”

Fact: Giving the Delta Smelt 1000 or 2000 cfs in June and July this year – instead of nothing (Delta outflow was allocated to repel salt) – would entail only 3-6% of the water released from reservoirs and 5-10% of Delta inflow. After all, the Delta Reform Act of 2009 mandates that the state must implement the “co-equal” goals of providing a reliable water supply and protecting, restoring and enhancing the Delta ecosystem.

Low Flows – Deadly Water Temperatures

Posted on August 22, 2016 by Tom Cannon

Low flows in the Sacramento River and Delta lead to deadly water temperatures for Central Valley salmon, steelhead, sturgeon, and smelt, including six state or federally listed endangered species. Water quality standards and operating requirements for the state and federal water projects should include new flow limits to protect fish.

Sacramento River

Salmon, steelhead, and sturgeon are subjected to deadly spring and summer water temperatures when lower Sacramento River flows fall below 5000 cfs as measured at Wilkins Slough (Figure 1). Low flows and high water temperatures lead to poor survival and increased predation, and block migrations of adult salmon.

Delta

Low flows through the lower Sacramento River channel in the Delta also lead to deadly water temperatures for salmon and smelt. When Delta inflow falls below 10,000 cfs, water temperatures become deadly for Delta Smelt (Figure 2) and salmon (Figure 3).

Figure 1. Daily average water temperature and river flow in the Sacramento River at Wilkins Slough (RM 125) 2007-2016. Water temperatures greater than 75°F are lethal to salmon and sturgeon, and block salmon migration. The water quality standard for the lower Sacramento River is a limit of 68°F. Temperatures above 68°F are stressful to salmon, sturgeon, and steelhead, and lead to increased risk of predation, lower survival, and poor reproductive success.

Figure 2. Daily average water temperature and river flow in lower Sacramento River near Freeport. Water temperatures greater than 73°F are lethal to smelt and block salmon migrations.

Figure 3. Daily average water temperature in the south Delta at Clifton Court 2009-2016. Water temperatures greater than 25°C (77°F) are lethal to salmon and smelt.

Smelt Extinction and Recovery: The Path Forward

Posted on August 11, 2016 by Tom Cannon

The March 29, 2016 Delta smelt symposium, part 4 (“Panel Discussion of the Path Forward”) offered some hope but few specific strategies for Bay-Delta smelt recovery. My own presentation and other presentations earlier in Part 2, focused on how smelt got to the brink of extinction. In Part 4, the panel of experts was asked to offer ways to bring smelt back from the brink. Reading the transcript and watching the video of the discussion, there did not appear to be any specific array of actions or coherent strategy offered by the panel. But on further review, I did find some nuggets that when put together sketch a reasonable course of action.

First, though, it is important to point out that over the past two decades there were two episodes that stopped extinction and brought some (albeit modest and short-lived) recovery with the help of Mother Nature. The D-1641 water quality standards and the actions required by the Delta Smelt Biological Opinion actions did help. The symposium should have focused more on those actions that helped, in order to see what further is needed. Admittedly, the fact that recovery episodes were not more frequent makes this difficult. It also does not speak well for 20 years of Bay-Delta adaptive management, which in large measure was a test to see how far the Bay-Delta ecosystem could be stressed by taking more and more water without breaking it. Now that the ecosystem is broken, it is harder to see what helps and what does not.

Here is what I assembled from the panel’s discussion as a reasonable strategy to put the smelt and the Bay-Delta ecosystem back on a recovery course again.

Yolo Bypass – Cache Slough Complex

Simply putting more Sacramento River water down the Bypass might improve the Complex and transfer more of its nutrients, turbidity, and plankton (and smelt) to the north Delta and eastern Bay low salinity zone. Available water sources include the Colusa Basin Drain and Fremont Weir. The large Sacramento River agricultural diversions that feed the Drain are minimally used outside the April-October irrigation season. Present mandates and plans to notch the Fremont Weir would provide a direct source of Sacramento River water to the Bypass. A long-mandated relocation of the North Bay Aqueduct intake from the Cache Slough Complex to the Sacramento River would also help.

Sacramento Deep Water Ship Channel

Mentioned several times as the last refuge of Delta smelt, the Ship Channel from the Port in West Sacramento to the lower end of Cache Slough offers potential in improving conditions for smelt. The closed gate at the upper end of the Ship Channel could be opened at key times to pass Sacramento River water into the upper channel to help flush smelt and nutrients into the north Delta, or simply to enhance smelt survival in the channel itself and in the lower Cache Slough Complex. A panelist suggested dredging the channel. Opening it in summer would cool the channel and possibly the lower Complex because the opening is near the mouth of the American River with its cool outflow.

Nutrients

The Panel suggested Increasing nutrients, specifically nitrogen, as a means of boosting plankton productivity and smelt survival in the Delta. Ironically, the Sac Regional Treatment Plant is being forced to reduce its ammonia and nitrogen inputs to the Delta. But the suggestion holds much promise because plankton blooms and turbidity from them are necessary staples of smelt critical habitat. A recent spring plankton bloom coincident with a San Joaquin River flow pulse and low Delta exports suggests one option for increasing nutrients and plankton blooms. Another option is the above-mentioned flow through the Bypass and Ship Channel. Not exporting higher nutrient low salinity zone water is another. Employing the Head of Old River Barrier would force more of the high nutrient San Joaquin water into the Central Delta and away from the south Delta export pumps.

More Delta Outflow to the Bay

Almost everyone on the panel suggested the need for more flow to the Bay to help the smelt. The smelt are simply far better off in wet years. But no one on the panel suggested upgrading the Delta Outflow requirements in the Bay-Delta D-1641 water quality standards, a process that has been ongoing for nearly a decade. Relaxation of the outflow requirements in the past four years of drought proved disastrous for smelt, the kind of adaptive management experiment we could do without. More outflow moves smelt into better habitat in Suisun Bay and Marsh. It also keeps them away from the export pumps, Delta agricultural diversions, and the warmer lower-turbidity confines of the Delta channels with their profusion of warm water competitors and predators. A panel member noted the difficulty of “finding” more water for outflow. The water is there; the need to is export less of it.

Exports

Several panelists suggested there has been too much emphasis on Delta exports, and that we should be focusing more on other solutions like improving habitats. While physical habitat improvements could help, the fact is that Delta pelagic habitat so essential to smelt and other Delta fishes has been severely degraded by exports (and lower outflows) at an ever increasing rate over the past four decades. Global warming is further adding to the stress. None of the panelists mentioned the benefits of export restrictions in the D-1641 standards or biological opinions. The agricultural community screams to weaken these restrictions, in part from the lack of recognition of their benefits.

Hatchery

Several panelists expressed the opinion that the species is protected from extinction by holding them in captivity in two conservation hatcheries. While that may be noble, it is not going to save the Delta or smelt. The option of expansion to production hatcheries was barely discussed, because of an underlying concern of where to put the hatchery fish given the poor existing habitat. But one panelist suggested stocking may be necessary to provide enough natural spawners to allow them to find one another during the spring spawn. Regardless, there are times and places where better habitat occurs such that if more smelt were added, it would benefit the population (e.g., when X2 is downstream of the Delta in the fall).

Predators

The panel mentioned predators, but only as one of the negative changes that have occurred over the past several decades. The panel discussed habitat enhancements as a means of reducing predators or their access to smelt. There was mention of increasing nutrients to increase phytoplankton food and turbidity, to shade out aquatic plants that shield non-native predator fishes. This holds promise if export operations do not replace good spatial habitat with incoming warm low turbidity river and reservoir water. The panel thankfully did not speak of directly removing Delta predators as a solution to the problem, a suggestion fostered by the ag community.

The Solution Package

As a group, the strategies mentioned above offer a reasonable short-term solution package to save the Delta smelt. Nearly all the actions can be immediately implemented, or at least started. As a followup to the symposium, I suggest a workshop to develop a plan for such a solution package to guide recovery during the coming years of water battles over the WaterFix (Delta Tunnels), the update of the Bay-Delta Water Quality Control Plan, and the revision of the biological opinions for the long-term operation of the CVP and SWP.

Delta Update – August 1, 2016

Posted on August 1, 2016 by Tom Cannon

Just a quick update on Delta fisheries on August 1, 2016. Delta outflow this spring-summer for this below-normal water year was as expected, except for the pulse of up to 14,000 cfs in the July experiment to help Delta Smelt (Figure 1). Year 2000, an above-normal year and a pre-Pelagic Organism Decline year, is shown for comparison.

Figure 1. Delta outflow May-July 2000 and 2016.

Striped Bass

My earlier optimism for this year’s striped bass production continues to fade. I continue to believe that the poor success is related to poor early summer Delta outflow based on comparison with year 2000, the last decent year class produced by striped bass in the Bay-Delta as determined by the June Summer Townet Survey. Figures 2 and 3 show abundance and distribution in 2000 and 2016, respectively. Densities were an order of magnitude higher in 2000, after spring larvae abundances were similar between the two years. Figures 4 and 5 show spring-summer salvage at south Delta pumps for 2000 and 2016, respectively. Again, much higher salvage in 2000 reflects the order of magnitude greater abundance in 2000 than in 2016.

Delta Smelt

Delta Smelt continue to be virtually extinct in the Bay-Delta. Figures 6 and 7 show abundance and distribution in 2000, the last near normal abundance year (pre-Pelagic Organism Decline), and 2016, respectively. Figures 8 and 9 show spring-summer salvage at south Delta pumps for 2000 and 2016, respectively. The relatively high salvage in 2000 reflects the general abundance at the end of the 90’s. The fact that there are no longer Delta Smelt in the 2016 Townet Survey or in salvage is a very clear indication that Delta Smelt are virtually extinct. The July experiment, though well intended, was a little too late.